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gag_polyprotein
Euk-VirAvian_leukemia_virus
gag_polyprotein__YP_004222727__Avian_leukemia_virus__11946
Identity
- Accession:
- YP_004222727 ↗
- Protein ID:
- gag_polyprotein
- Kingdom:
- euk
Quality
59.8
mean pLDDT
Taxonomy
Pararnavirae›
Artverviricota›
Revtraviricetes›
Ortervirales›
Retroviridae›
Alpharetrovirus›
Avian_leukemia_virus
TaxID: 11946
Cluster
Singleton — not in a non-trivial cluster
3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
high
residues 1-97
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02813.19 best | Retro_M | 191.0 | 4.60e-57 | 88.7% | 100.0% |
CATH (34)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3nbiA01 | 1.10.8.1020 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › RecQ-mediated genome instability protein 1, N-terminal domain | 0.69 | 40.0 | 4.96e-01 | 78.4% | 96.6% |
| 4lqkA00 | 1.10.437.20 | Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › dsDNA poxvirus | 0.63 | 47.0 | 4.23e-01 | 78.4% | 57.6% |
| 1c9bA01 | 1.10.472.10 | Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like | 0.62 | 43.0 | 4.39e-01 | 73.2% | 96.9% |
| 2go7A02 | 1.10.150.240 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 | 0.62 | 39.0 | 4.56e-01 | 100.0% | 92.5% |
| 1aueB00 | 1.20.120.150 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › FKBP12-rapamycin binding domain | 0.62 | 42.0 | 4.33e-01 | 71.1% | 80.9% |
| 3iqcA00 | 1.20.120.340 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS | 0.61 | 45.0 | 4.21e-01 | 78.4% | 82.4% |
| 3r2cA00 | 1.10.940.10 | Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like | 0.60 | 48.0 | 4.30e-01 | 90.7% | 61.6% |
| 2kiwA01 | 1.10.150.130 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain | 0.60 | 46.0 | 4.85e-01 | 89.7% | 96.5% |
| 1aisB01 | 1.10.472.10 | Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like | 0.59 | 42.0 | 4.23e-01 | 74.2% | 98.0% |
| 2lseA00 | 1.20.120.1360 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › | 0.58 | 47.0 | 4.67e-01 | 85.6% | 83.2% |
| 1tjoB00 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.57 | 47.0 | 3.96e-01 | 91.8% | 76.0% |
| 1ax8A00 | 1.20.1250.10 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › | 0.57 | 48.0 | 4.35e-01 | 92.8% | 95.4% |
| 2cmrA00 | 1.20.58.1860 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.56 | 48.0 | 3.83e-01 | 92.8% | 91.1% |
| 2bvlA01 | 1.20.58.1190 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.56 | 46.0 | 4.86e-01 | 91.8% | 100.0% |
| 6adqG01 | 1.20.120.80 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c oxidase, subunit III, four-helix bundle | 0.56 | 47.0 | 3.91e-01 | 93.8% | 87.1% |
| 4gr2A00 | 1.10.1200.210 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Chaperonin-like RbcX | 0.56 | 40.0 | 3.91e-01 | 91.8% | 67.3% |
| 4rngC00 | 1.20.1280.290 | Mainly Alpha › Up-down Bundle › Monooxygenase › | 0.55 | 39.0 | 4.14e-01 | 89.7% | 84.3% |
| 2gs4A00 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.55 | 46.0 | 3.97e-01 | 92.8% | 86.7% |
| 2pjqA01 | 1.10.472.50 | Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › HD-domain/PDEase-like | 0.55 | 39.0 | 4.10e-01 | 99.0% | 83.1% |
| 3v53E00 | 1.20.1390.10 | Mainly Alpha › Up-down Bundle › PWI domain › PWI domain | 0.55 | 39.0 | 3.86e-01 | 90.7% | 70.6% |
| 2hsbA00 | 1.20.120.330 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 | 0.55 | 44.0 | 4.06e-01 | 90.7% | 67.5% |
| 2vxxA00 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.55 | 47.0 | 3.88e-01 | 93.8% | 76.7% |
| 2c41C01 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.55 | 46.0 | 4.04e-01 | 93.8% | 87.9% |
| 2c2uA00 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.54 | 46.0 | 3.79e-01 | 93.8% | 74.2% |
| 1u8vA01 | 1.10.3140.10 | Mainly Alpha › Orthogonal Bundle › 4-hydroxybutyryl-coa dehydratase, domain 1 › 4-hydroxybutyryl-coa dehydratase, domain 1 | 0.54 | 47.0 | 4.20e-01 | 100.0% | 93.7% |
| 2ouwB00 | 1.20.1290.10 | Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like | 0.54 | 41.0 | 3.68e-01 | 85.6% | 58.1% |
| 1cnt200 | 1.20.1250.10 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › | 0.53 | 46.0 | 4.16e-01 | 93.8% | 93.8% |
| 3if8B02 | 1.20.58.730 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.52 | 31.0 | 3.12e-01 | 90.7% | 55.0% |
| 2hjmA01 | 1.20.120.460 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › protein pf1176 like | 0.52 | 43.0 | 4.50e-01 | 90.7% | 100.0% |
| 3ed5A02 | 1.10.150.240 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 | 0.52 | 41.0 | 4.30e-01 | 100.0% | 98.8% |
| 3iq1B00 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.52 | 43.0 | 3.75e-01 | 93.8% | 80.5% |
| 2bl7A00 | 1.20.1440.50 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like | 0.52 | 38.0 | 4.15e-01 | 81.4% | 96.2% |
| 1ng6A01 | 1.10.1510.10 | Mainly Alpha › Orthogonal Bundle › Hypothetical Protein Yqey; Chain: A; domain1 › Uncharacterised protein YqeY/AIM41, N-terminal domain | 0.51 | 37.0 | 3.81e-01 | 77.3% | 96.7% |
| 1g2nA00 | 1.10.565.10 | Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor | 0.51 | 42.0 | 3.27e-01 | 96.9% | 56.1% |
ECOD (36)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2095614 | 612.1.1.5 ↗ | alpha arrays › Retroviral matrix proteins › Retroviral matrix proteins › Retroviral matrix proteins › Retro_M | 0.93 | 90.0 | 8.73e-01 | 100.0% | 94.2% |
| 4936259 | 3930.1.1.3 ↗ | alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase › RNA_helicase_helical | 0.69 | 50.0 | 4.56e-01 | 86.6% | 57.6% |
| 4967419 | 3930.1.1.0 ↗ | alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase | 0.68 | 49.0 | 4.39e-01 | 87.6% | 54.1% |
| 3257419 | 174.1.1.0 ↗ | few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain | 0.66 | 52.0 | 4.89e-01 | 85.6% | 91.7% |
| 5066065 | 3930.1.1.3 ↗ | alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase › RNA_helicase_helical | 0.65 | 45.0 | 4.14e-01 | 89.7% | 55.2% |
| 4362692 | 186.1.1.1 ↗ | alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_1 | 0.64 | 53.0 | 5.29e-01 | 96.9% | 90.0% |
| 3228302 | 601.1.2.0 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) | 0.62 | 50.0 | 4.64e-01 | 85.6% | 96.7% |
| 3729395 | 633.21.1.0 ↗ | alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 | 0.62 | 50.0 | 4.56e-01 | 87.6% | 92.3% |
| 3580290 | 150.1.1.126 ↗ | alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › PF28643 | 0.61 | 51.0 | 4.20e-01 | 92.8% | 92.8% |
| 5019699 | 3755.3.1.0 ↗ | alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin | 0.60 | 50.0 | 4.00e-01 | 90.7% | 47.2% |
| 3670152 | 5069.1.3.24 ↗ | alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › TIC20 | 0.59 | 42.0 | 3.69e-01 | 73.2% | 77.2% |
| 9328 | 2003.1.5.75 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › AviRa | 0.58 | 47.0 | 3.49e-01 | 86.6% | 64.7% |
| 54315 | 633.16.1.0 ↗ | alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like | 0.58 | 47.0 | 4.87e-01 | 86.6% | 100.0% |
| 3627650 | 633.23.1.0 ↗ | alpha bundles › Bromodomain-like › Claudin › Claudin | 0.58 | 47.0 | 4.41e-01 | 87.6% | 88.3% |
| 5018283 | 633.10.1.0 ↗ | alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like | 0.58 | 47.0 | 4.75e-01 | 88.7% | 90.0% |
| 2074038 | 633.16.1.2 ↗ | alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like › TcdB_N | 0.57 | 46.0 | 4.84e-01 | 86.6% | 100.0% |
| 3599845 | 633.15.1.0 ↗ | alpha bundles › Bromodomain-like › alpha-ketoacid dehydrogenase kinase-N › alpha-ketoacid dehydrogenase kinase-N | 0.57 | 48.0 | 3.98e-01 | 92.8% | 90.9% |
| 3924586 | 633.21.1.0 ↗ | alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 | 0.57 | 46.0 | 4.08e-01 | 86.6% | 96.4% |
| 4856197 | 633.16.1.2 ↗ | alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like › TcdB_N | 0.57 | 46.0 | 4.43e-01 | 86.6% | 80.9% |
| 3930703 | 632.22.1.0 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats | 0.57 | 44.0 | 4.38e-01 | 83.5% | 91.0% |
| 3411467 | 633.23.1.42 ↗ | alpha bundles › Bromodomain-like › Claudin › Claudin › PF28643 | 0.56 | 45.0 | 3.20e-01 | 86.6% | 48.7% |
| 3231853 | 174.1.1.13 ↗ | few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › DUF2700 | 0.56 | 46.0 | 4.22e-01 | 88.7% | 91.2% |
| 3321734 | 633.1.1.0 ↗ | alpha bundles › Bromodomain-like › Bromodomain › Bromodomain | 0.56 | 49.0 | 4.64e-01 | 100.0% | 81.7% |
| 3242255 | 174.1.1.13 ↗ | few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › DUF2700 | 0.56 | 44.0 | 3.82e-01 | 87.6% | 82.3% |
| 3806415 | 4133.1.1.2 ↗ | alpha arrays › Emsy N terminal (ENT) domain-like › Emsy N terminal (ENT) domain-like › Emsy N terminal (ENT) domain-like › Tic110 | 0.55 | 36.0 | 3.47e-01 | 71.1% | 55.7% |
| 4862607 | 633.16.1.2 ↗ | alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like › TcdB_N | 0.54 | 43.0 | 4.45e-01 | 86.6% | 100.0% |
| 3954969 | 106.1.1.1 ↗ | alpha arrays › Globin-like › Globin-like › Globin-like › Globin | 0.54 | 41.0 | 3.75e-01 | 84.5% | 99.3% |
| 3262205 | 633.24.1.0 ↗ | alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain | 0.53 | 36.0 | 3.79e-01 | 70.1% | 87.8% |
| 3346956 | 103.1.1.0 ↗ | alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain | 0.53 | 44.0 | 4.51e-01 | 93.8% | 92.6% |
| 4360987 | 601.4.1.34 ↗ | alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains › SHR3_chaperone | 0.53 | 37.0 | 3.11e-01 | 72.2% | 65.1% |
| 4986068 | 5082.1.1.1 ↗ | alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux | 0.53 | 46.0 | 3.66e-01 | 95.9% | 79.5% |
| 4583117 | 3755.4.1.0 ↗ | alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain | 0.53 | 42.0 | 3.98e-01 | 86.6% | 75.8% |
| 4959669 | 2008.1.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like | 0.52 | 40.0 | 3.11e-01 | 85.6% | 66.7% |
| 4338795 | 192.2.1.0 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin | 0.52 | 44.0 | 3.65e-01 | 92.8% | 71.2% |
| 3394485 | 6155.1.1.1 ↗ | alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › MtN3_slv | 0.51 | 36.0 | 3.84e-01 | 88.7% | 84.7% |
| 3834324 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.50 | 45.0 | 2.93e-01 | 97.9% | 27.1% |
D2
high
residues 241-385
Domain cluster:
rep: gag_protein__YP_009305199__Simian_retrovirus_8__1904439__D302-440
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00607.26 best | Gag_p24 | 67.1 | 2.00e-18 | 94.5% | 96.1% |
CATH (20)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2kgfA00 | 1.10.375.10 | Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein | 0.74 | 64.0 | 6.53e-01 | 100.0% | 96.4% |
| 2xgvA00 | 1.10.375.10 | Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein | 0.73 | 61.0 | 6.39e-01 | 100.0% | 97.7% |
| 2xguB00 | 1.10.375.10 | Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein | 0.73 | 63.0 | 6.54e-01 | 100.0% | 99.3% |
| 1d1dA01 | 1.10.375.10 | Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein | 0.72 | 64.0 | 6.50e-01 | 93.8% | 97.1% |
| 1l6nA02 | 1.10.375.10 | Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein | 0.71 | 59.0 | 6.18e-01 | 90.3% | 97.7% |
| 1eiaA01 | 1.10.375.10 | Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein | 0.69 | 57.0 | 5.99e-01 | 92.4% | 96.2% |
| 1u7kA00 | 1.10.375.10 | Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein | 0.68 | 57.0 | 6.00e-01 | 99.3% | 99.2% |
| 2y1eA03 | 1.10.1740.10 | Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif | 0.65 | 29.0 | 3.67e-01 | 91.7% | 67.8% |
| 4px7A00 | 1.20.144.10 | Mainly Alpha › Up-down Bundle › Vanadium-containing Chloroperoxidase; domain 1 › Phosphatidic acid phosphatase type 2/haloperoxidase | 0.60 | 45.0 | 3.74e-01 | 78.6% | 88.8% |
| 2w31A00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.55 | 43.0 | 4.29e-01 | 93.1% | 78.9% |
| 2gtaA00 | 1.10.287.1080 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like | 0.55 | 28.0 | 3.38e-01 | 89.0% | 73.2% |
| 3qbmB00 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.54 | 39.0 | 3.60e-01 | 75.2% | 87.8% |
| 3gi7A00 | 1.20.1270.180 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.54 | 36.0 | 4.10e-01 | 98.6% | 95.1% |
| 3ubcA00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.53 | 38.0 | 4.04e-01 | 91.0% | 82.4% |
| 5b2nA00 | 1.20.1070.10 | Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins | 0.52 | 42.0 | 3.44e-01 | 84.8% | 80.2% |
| 1at9A00 | 1.20.1070.10 | Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins | 0.51 | 41.0 | 3.53e-01 | 84.8% | 87.4% |
| 3cbfA01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.51 | 37.0 | 3.46e-01 | 97.9% | 61.1% |
| 3s0xA01 | 1.20.120.1220 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › | 0.51 | 37.0 | 3.69e-01 | 75.9% | 73.5% |
| 3b5oA00 | 1.20.910.10 | Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like | 0.51 | 45.0 | 3.91e-01 | 98.6% | 96.5% |
| 3b9wA00 | 1.10.3430.10 | Mainly Alpha › Orthogonal Bundle › Ammonium transporter fold › Ammonium transporter AmtB like domains | 0.50 | 45.0 | 3.41e-01 | 99.3% | 78.7% |
ECOD (17)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 56909 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.81 | 75.0 | 7.46e-01 | 97.2% | 97.3% |
| 3866760 | 170.2.1.1 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24 | 0.79 | 69.0 | 7.06e-01 | 100.0% | 95.7% |
| 3543503 | 170.2.1.1 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24 | 0.75 | 71.0 | 6.90e-01 | 100.0% | 96.2% |
| 1678502 | 170.2.1.1 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24 | 0.75 | 70.0 | 6.52e-01 | 99.3% | 97.2% |
| 145205 | 170.2.1.1 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24 | 0.74 | 68.0 | 6.73e-01 | 100.0% | 96.0% |
| 2126757 | 170.2.1.1 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24 | 0.74 | 64.0 | 6.53e-01 | 100.0% | 96.4% |
| 140763 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.73 | 61.0 | 6.39e-01 | 100.0% | 97.7% |
| 2138586 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.73 | 63.0 | 6.49e-01 | 100.0% | 95.7% |
| 56881 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.72 | 66.0 | 6.68e-01 | 100.0% | 98.6% |
| 140713 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.72 | 64.0 | 6.44e-01 | 100.0% | 95.8% |
| 4057 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.70 | 58.0 | 6.09e-01 | 91.7% | 96.9% |
| 3239947 | 5067.1.1.2 ↗ | alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › SecD_SecF | 0.61 | 35.0 | 2.99e-01 | 95.9% | 35.1% |
| 3288489 | 620.1.1.6 ↗ | alpha bundles › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › DinB_2 | 0.56 | 44.0 | 4.24e-01 | 82.1% | 73.9% |
| 4673693 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.55 | 49.0 | 4.20e-01 | 100.0% | 80.0% |
| 3734736 | 3684.1.1.22 ↗ | alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › Opi1 | 0.51 | 40.0 | 3.99e-01 | 83.4% | 89.7% |
| 3616362 | 109.46.1.1 ↗ | alpha superhelices › Repetitive alpha hairpins › Helical domain in TOPLESS related protein 2 (TPR2) › Helical domain in TOPLESS related protein 2 (TPR2) › CTLH | 0.51 | 40.0 | 4.06e-01 | 81.4% | 97.9% |
| 5019493 | 604.39.1.0 ↗ | alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters | 0.50 | 43.0 | 3.80e-01 | 94.5% | 63.6% |
D3
high
residues 589-694
Domain cluster:
rep: protease,_partial__YP_009305200__Simian_retrovirus_8__1904439__D173-265
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00077.26 best | RVP | 87.7 | 7.70e-25 | 100.0% | 89.1% |
D4
medium
residues 388-464
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF19317.5 best | Gag_p24_C | 26.3 | 6.90e-06 | 93.5% | 79.7% |
CATH (26)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1d1dA02 | 1.10.1200.30 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Retrovirus capsid C-terminal domain | 0.93 | 86.0 | 8.54e-01 | 98.7% | 93.8% |
| 1bajA00 | 1.10.1200.30 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Retrovirus capsid C-terminal domain | 0.85 | 72.0 | 7.53e-01 | 94.8% | 100.0% |
| 5dckA00 | 1.10.1200.30 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Retrovirus capsid C-terminal domain | 0.84 | 71.0 | 7.36e-01 | 98.7% | 97.2% |
| 1qrjA02 | 1.10.1200.30 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Retrovirus capsid C-terminal domain | 0.78 | 70.0 | 6.77e-01 | 98.7% | 89.4% |
| 4l8iB00 | 1.10.132.20 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor | 0.71 | 48.0 | 4.27e-01 | 70.1% | 87.5% |
| 1j8yF01 | 1.20.120.140 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain | 0.68 | 50.0 | 4.93e-01 | 80.5% | 97.7% |
| 4uqfA02 | 3.30.1130.10 | Alpha Beta › 2-Layer Sandwich › GTP Cyclohydrolase I, domain 2 › GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain | 0.65 | 51.0 | 4.20e-01 | 83.1% | 97.8% |
| 1ls1A01 | 1.20.120.140 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain | 0.64 | 49.0 | 4.71e-01 | 84.4% | 94.4% |
| 1iqpA03 | 1.20.272.10 | Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › | 0.64 | 53.0 | 5.02e-01 | 94.8% | 96.8% |
| 2xheA04 | 1.25.40.60 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › | 0.63 | 44.0 | 3.89e-01 | 89.6% | 48.3% |
| 3b0pA02 | 1.20.120.1460 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › | 0.59 | 46.0 | 4.68e-01 | 85.7% | 92.0% |
| 2mabA00 | 1.10.10.1350 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Spidroin domain, C-terminal domain | 0.59 | 51.0 | 4.59e-01 | 96.1% | 87.2% |
| 2o38A01 | 1.10.260.40 | Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains | 0.58 | 35.0 | 3.78e-01 | 80.5% | 70.8% |
| 6vvoC03 | 1.20.272.10 | Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › | 0.58 | 49.0 | 4.72e-01 | 100.0% | 100.0% |
| 7qocA01 | 1.10.3210.10 | Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 | 0.57 | 40.0 | 3.11e-01 | 75.3% | 31.6% |
| 3cz6A01 | 1.20.120.1480 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › | 0.56 | 44.0 | 4.05e-01 | 89.6% | 64.4% |
| 4ga6A02 | 1.20.970.50 | Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › | 0.55 | 40.0 | 3.28e-01 | 88.3% | 40.1% |
| 3b9qA01 | 1.20.120.140 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain | 0.54 | 42.0 | 4.08e-01 | 85.7% | 89.9% |
| 3ea5D00 | 1.25.10.10 | Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant | 0.54 | 42.0 | 2.41e-01 | 85.7% | 8.4% |
| 1juqC00 | 1.25.40.90 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › | 0.53 | 42.0 | 3.52e-01 | 90.9% | 96.6% |
| 4jgwA01 | 1.20.870.10 | Mainly Alpha › Up-down Bundle › Son of sevenless (SoS) protein; Chain S, domain 1 › Son of sevenless (SoS) protein Chain: S domain 1 | 0.52 | 44.0 | 3.60e-01 | 98.7% | 73.1% |
| 2ex2A01 | 3.40.710.10 | Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily | 0.52 | 39.0 | 2.80e-01 | 81.8% | 37.1% |
| 3hhsA01 | 1.20.1370.10 | Mainly Alpha › Up-down Bundle › Hemocyanin, N-terminal domain › Hemocyanin, N-terminal domain | 0.51 | 40.0 | 3.38e-01 | 89.6% | 51.0% |
| 4g26A01 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.51 | 44.0 | 3.00e-01 | 100.0% | 30.3% |
| 3od1A01 | 3.30.930.10 | Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 | 0.50 | 41.0 | 2.79e-01 | 93.5% | 85.6% |
| 3tjzB00 | 1.25.10.10 | Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant | 0.50 | 38.0 | 2.76e-01 | 85.7% | 38.6% |
ECOD (45)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2733984 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.97 | 90.0 | 8.98e-01 | 96.1% | 94.9% |
| 3896 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.93 | 86.0 | 8.54e-01 | 98.7% | 93.8% |
| 3841386 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.89 | 61.0 | 7.20e-01 | 71.4% | 100.0% |
| 4892091 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.88 | 62.0 | 6.48e-01 | 72.7% | 78.9% |
| 3510249 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.86 | 76.0 | 7.10e-01 | 100.0% | 78.5% |
| 2984623 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.85 | 78.0 | 7.25e-01 | 98.7% | 84.2% |
| 55547 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.84 | 68.0 | 7.15e-01 | 93.5% | 95.7% |
| 3746214 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.84 | 75.0 | 7.62e-01 | 97.4% | 98.7% |
| 4400236 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.84 | 77.0 | 6.88e-01 | 100.0% | 85.7% |
| 3480818 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.83 | 69.0 | 6.66e-01 | 90.9% | 80.0% |
| 3515443 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.83 | 75.0 | 7.12e-01 | 100.0% | 83.3% |
| 2797120 | 170.1.1.22 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › PF30901 | 0.83 | 73.0 | 6.85e-01 | 100.0% | 80.2% |
| 3845048 | 170.1.1.25 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › PNMA | 0.82 | 76.0 | 6.76e-01 | 100.0% | 82.9% |
| 3896388 | 170.1.1.22 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › PF30901 | 0.81 | 71.0 | 6.72e-01 | 100.0% | 81.1% |
| 3941114 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.81 | 70.0 | 6.92e-01 | 93.5% | 100.0% |
| 3199067 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.81 | 71.0 | 6.80e-01 | 98.7% | 83.1% |
| 3633075 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.81 | 74.0 | 7.05e-01 | 100.0% | 87.8% |
| 2568930 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.81 | 71.0 | 6.80e-01 | 97.4% | 84.1% |
| 2568911 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.80 | 72.0 | 6.71e-01 | 98.7% | 84.9% |
| 3518742 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.79 | 72.0 | 7.03e-01 | 100.0% | 95.3% |
| 1175290 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.78 | 69.0 | 6.76e-01 | 97.4% | 89.3% |
| 3930503 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.78 | 71.0 | 6.63e-01 | 100.0% | 85.3% |
| 3762196 | 170.1.1.22 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › PF30901 | 0.78 | 70.0 | 6.68e-01 | 100.0% | 84.4% |
| 3816443 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.78 | 67.0 | 6.78e-01 | 100.0% | 97.3% |
| 3631496 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.78 | 69.0 | 6.41e-01 | 98.7% | 78.9% |
| 3632068 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.76 | 54.0 | 5.95e-01 | 75.3% | 95.0% |
| 3937617 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.76 | 66.0 | 6.42e-01 | 97.4% | 91.8% |
| 3926116 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.74 | 66.0 | 6.17e-01 | 100.0% | 88.4% |
| 3460605 | 170.2.1.12 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Retrotrans_gag | 0.73 | 65.0 | 6.36e-01 | 100.0% | 98.8% |
| 3929266 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.73 | 55.0 | 5.39e-01 | 80.5% | 75.3% |
| 3937527 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.73 | 65.0 | 6.04e-01 | 98.7% | 86.3% |
| 3941254 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.73 | 64.0 | 5.99e-01 | 100.0% | 87.4% |
| 3409030 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.72 | 63.0 | 6.43e-01 | 100.0% | 100.0% |
| 3935441 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.72 | 60.0 | 5.96e-01 | 96.1% | 90.0% |
| 4013028 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.71 | 62.0 | 5.48e-01 | 100.0% | 87.8% |
| 3775745 | 170.1.1.29 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › DUF5535 | 0.68 | 59.0 | 4.60e-01 | 98.7% | 52.6% |
| 3507225 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.66 | 52.0 | 5.47e-01 | 90.9% | 100.0% |
| 3193662 | 592.1.1.1 ↗ | alpha arrays › PWI domain-like › PWI domain › PWI domain › PWI | 0.62 | 42.0 | 4.23e-01 | 71.4% | 81.2% |
| 3218479 | 4156.1.1.4 ↗ | alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › HA2_C | 0.58 | 50.0 | 4.05e-01 | 98.7% | 83.2% |
| 3710692 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.57 | 47.0 | 3.12e-01 | 98.7% | 19.7% |
| 3966605 | 601.4.1.84 ↗ | alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains › KinB_sensor | 0.54 | 42.0 | 3.71e-01 | 87.0% | 80.0% |
| 3442806 | 2007.5.1.1 ↗ | a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL | 0.54 | 45.0 | 2.97e-01 | 94.8% | 47.4% |
| 3499486 | 109.4.1.170 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CLASP_N | 0.53 | 40.0 | 2.81e-01 | 85.7% | 35.3% |
| 3695528 | 109.3.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat | 0.52 | 40.0 | 3.05e-01 | 84.4% | 62.6% |
| 3936737 | 150.1.1.0 ↗ | alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin | 0.50 | 44.0 | 3.21e-01 | 100.0% | 64.5% |